SHRiMP v2.2.3

SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.

Accessing the software

To load the module:

$ module load apps/shrimp/v2.2.3

An example command to include in your job script:

gmapper-cs 0_to_2499999.csfasta ciona.fa -N 16 -o 5 -h 80% >map.0_to_2499999.out \
      2>map.0_to_2499999.log

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

  • Threaded parallelism, using multiple cores on a node, is supported as shown in the previous example. Distributed memory parallelism, using multiple nodes, is not available in SHRiMP.

Other Information

The Support Level for this application is An.

Visit the SHRiMP website for more information regarding this application.


Last modified: 8 December 2017